Beyond biology: Simple system yields custom-designed proteins

PRINCETON, N.J. -- The diversity of nature may be enormous, but for Michael Hecht it is just a starting point.

Hecht, a Princeton professor of chemistry, has invented a technique for making protein molecules from scratch, a long-sought advance that will allow scientists to design the most basic building blocks of all living things with a variety of shapes and compositions far greater than those available in nature.

The technique, which Hecht developed over the last 10 years and validated in experiments to be published in November, could prove useful in a wide range of fields. Custom-designed proteins, for example, could become a source of new drugs or could form the basis of new materials that mimic the strength and resilience of natural substances.

The range of proteins present in nature, while great, has evolved only as far as the needs of biological organisms, said Hecht. "Why should we be limited by a mere few million proteins?" he said. "We can now not only ask what already exists in the biological world, but go beyond that and ask what might be possible."

Hecht and colleagues from Princeton and Rutgers University reported the advance in a paper to be published Nov. 11 in the Proceedings of the National Academy of Sciences. Co-authors of the article are former Princeton graduate student Yinan Wei and Rutgers chemistry professor Jean Baum and her colleagues Seho Kim and David Fela.

Nearly all the internal workings of living things are built from proteins. While genes are the "blueprints" for organisms, proteins are the products built from those instructions. The molecules that transmit signals in the brain, carry oxygen in the blood and turn genes on and off are all proteins.

Scientists have long wanted to design their own proteins, but doing so has proved a major challenge. Proteins are strings of chemical units called amino acids and are often more than 100 amino acids long. When cells make them, these long chains fold spontaneously into complex three-dimensional shapes that fit like puzzle pieces with other molecules and give proteins their unique abilities. There are 20 different amino acids, so the number of possible combinations is enormous. However, the vast majority of these combinations are useless because they cannot fold into protein-like structures.

The advance reported by Hecht and colleagues involves a simple system for designing amino acid sequences that fold like natural proteins. First publishing the idea in 1993, Hecht realized that some amino acids were strongly "water-loving" while others were "oil-loving." The two types naturally separate from each other, with the oil-loving ones clustering in the protein core and water-loving ones forming the perimeter. He also saw that natural proteins with good structures tend to have certain repeating patterns of oil-loving and water-loving amino acids. For example, taking a string of water-loving units -- no matter which ones -- and inserting any oil-loving unit every three or four positions typically creates proteins that fold into bundles of helices.

Hecht used this method to create a "library" of genes encoding millions of novel proteins, each designed to fold into a bundle of four helices. Initial tests of the library in the early 1990s showed that most of the proteins folded into compact arrangements, but these were "mushy," fluctuating shapes instead of well-ordered, rigid structures.

Hecht suspected that these proteins were simply too short to achieve a good structure and added amino acids to each sequence, making them 40 percent longer. In their latest findings, the researchers found that this new library contained well-folded proteins. They subjected one to a painstaking test -- a type of MRI for molecules -- and verified its three-dimensional structure. The experimentally determined structure closely matches that expected from the design.

The results are "quite important work," according to Jane Richardson, a biochemist at Duke University, and are a "direct demonstration of the importance of one simple and central factor in protein folding, which has not in the past been much emphasized in either the design or the folding fields."

Previously, the only ways for scientists to invent new proteins have been to churn out random sequences and screen them for well-folded proteins or to calculate, atom-by-atom, combinations that will fold into a desired shape. The first is difficult because there are too many combinations to try them all, said Hecht. Making every possible sequence of 100 amino acids would require more than all the atoms in universe, he said. The second, the calculation method, yields only one protein at a time.

Hecht's method offers a middle ground because it limits the number of possible sequences to those that fit the correct oil-loving/water-loving patterns.

Having a rich variety of custom proteins may allow scientists to consider using them for tasks that do not exist in nature, such as catalyzing industrial chemical reactions, Hecht said. "Critters in nature haven't been challenged to solve the technological problems we're faced with today," he said. "If we are limited by what nature has given us, we are not going to tackle those problems."